Reading "sample.raw" fails

[breidan]

Hi,
after migration to R4.5 and updating my BioConcductor packages rawrr is not working anymore. Issueing H <- rawrr::readFileHeader(rawfile = sampleFilePath()) throws the following error:

GC heap initialization failed with error 0x8007000E
Failed to create CoreCLR, HRESULT: 0x8007000E
Error in if (rvs != "No RAW file specified!") { :
argument is of length zero
In addition: Warning message:
In system2(exe, stdout = TRUE) :
running command ''/R/rawrr/rawrrassembly/linux-x64/rawrr'' had status 137

Mono is in the path:

Sys.which("mono")
mono
"/usr/bin/mono"

The rawrr assembly is installed:

list.files(rawrrAssemblyPath())
[1] "rawrr"

And here is the sessionInfo:

sessionInfo()
R version 4.5.0 (2025-04-11)
Platform: x86_64-pc-linux-gnu
Running under: Red Hat Enterprise Linux 9.6 (Plow)

Matrix products: default
BLAS/LAPACK: /usr/lib64/libopenblas-r0.3.26.so; LAPACK version 3.12.0

locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
[4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

time zone: Europe/Rome
tzcode source: system (glibc)

attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods base

other attached packages:
[1] MsBackendRawFileReader_1.14.0 Spectra_1.18.2
[3] S4Vectors_0.46.0 BiocGenerics_0.54.0
[5] generics_0.1.3 MsExperiment_1.10.0
[7] ProtGenerics_1.40.0 ABs.xcmsHelpers_1.8
[9] xcms_4.6.0 BiocParallel_1.42.1
[11] rawrr_1.16.0 lubridate_1.9.4
[13] forcats_1.0.0 stringr_1.5.1
[15] dplyr_1.1.4 purrr_1.0.4
[17] readr_2.1.5 tidyr_1.3.1
[19] tibble_3.2.1 tidyverse_2.0.0
[21] ggrepel_0.9.6 ggplot2_3.5.2
[23] magrittr_2.0.3 MUtools_1.4
[25] MASS_7.3-65

loaded via a namespace (and not attached):
[1] DBI_1.2.3 rlang_1.1.6 clue_0.3-66
[4] MassSpecWavelet_1.74.0 matrixStats_1.5.0 compiler_4.5.0
[7] vctrs_0.6.5 reshape2_1.4.4 pkgconfig_2.0.3
[10] MetaboCoreUtils_1.16.1 crayon_1.5.3 fastmap_1.2.0
[13] XVector_0.48.0 rmarkdown_2.29 pracma_2.4.4
[16] tzdb_0.5.0 preprocessCore_1.70.0 UCSC.utils_1.4.0
[19] xfun_0.52 MultiAssayExperiment_1.34.0 GenomeInfoDb_1.44.0
[22] jsonlite_2.0.0 progress_1.2.3 DelayedArray_0.34.1
[25] prettyunits_1.2.0 parallel_4.5.0 cluster_2.1.8.1
[28] R6_2.6.1 stringi_1.8.7 RColorBrewer_1.1-3
[31] limma_3.64.1 pkgload_1.4.0 GenomicRanges_1.60.0
[34] iterators_1.0.14 Rcpp_1.0.14 SummarizedExperiment_1.38.1
[37] knitr_1.50 IRanges_2.42.0 BiocBaseUtils_1.10.0
[40] Matrix_1.7-3 igraph_2.1.4 timechange_0.3.0
[43] tidyselect_1.2.1 rstudioapi_0.17.1 abind_1.4-8
[46] yaml_2.3.10 doParallel_1.0.17 codetools_0.2-20
[49] affy_1.86.0 lattice_0.22-6 plyr_1.8.9
[52] Biobase_2.68.0 withr_3.0.2 evaluate_1.0.3
[55] pillar_1.10.2 affyio_1.78.0 BiocManager_1.30.25
[58] MatrixGenerics_1.20.0 rsconnect_1.3.4 foreach_1.5.2
[61] MSnbase_2.34.1 MALDIquant_1.22.3 ncdf4_1.24
[64] hms_1.1.3 munsell_0.5.1 scales_1.3.0
[67] glue_1.8.0 MsFeatures_1.16.0 lazyeval_0.2.2
[70] tools_4.5.0 mzID_1.46.0 QFeatures_1.18.0
[73] vsn_3.76.0 mzR_2.42.0 XML_3.99-0.18
[76] fs_1.6.6 grid_4.5.0 impute_1.82.0
[79] MsCoreUtils_1.20.0 colorspace_2.1-1 GenomeInfoDbData_1.2.14
[82] PSMatch_1.12.0 cli_3.6.4 S4Arrays_1.8.1
[85] AnnotationFilter_1.32.0 pcaMethods_2.0.0 gtable_0.3.6
[88] digest_0.6.37 SparseArray_1.8.0 htmltools_0.5.8.1
[91] lifecycle_1.0.4 httr_1.4.7 statmod_1.5.0

Any help is much appreciated.

[breidan]

Any thoughts on the above? I would really need to use MsBackendRawFileReader and that won't work without rawrr.

Cheers
Andreas

[cpanse]

@breidan, the snippet below should solve the issue.

install.packages('https://fgcz-ms.uzh.ch/~cpanse/rawrr/rawrr_1.17.2.tar.gz')
library(rawrr)
rawrr::installRawrrExe(force = T)

[breidan]

@cpanse, thanks for the reply. But it did not solve the problem. Even with rawrr_1.17.2 and its assembly I get the same error message.

[cpanse]

@breidan can you send me the session info again? of note, rawrr 1.17 ships with a static compiled file.

[breidan]

@cpanse,

here is the whole command sequence:

library(rawrr)
rawrr::installRawrrExe(force = T)
Assembly exists. Do you want to overwrite it? [Y/n]: Y
Overwrite sourceUrl to https://fgcz-ms.uzh.ch/~cpanse/rawrr/dotnet/1.17.2//linux-x64/rawrr
trying URL 'https://fgcz-ms.uzh.ch/~cpanse/rawrr/dotnet/1.17.2//linux-x64/rawrr'
Content type 'unknown' length 117270765 bytes (111.8 MB)
==================================================
downloaded 111.8 MB

MD5 0e9739572de330e5b04671727ddc9adc /delta/JRC/services/rstudio-home/breidan@delta.europa.eu/.cache/R/rawrr/rawrrassembly/linux-x64/rawrr
[1] 0
H <- rawrr::readFileHeader(rawfile = sampleFilePath())
GC heap initialization failed with error 0x8007000E
Failed to create CoreCLR, HRESULT: 0x8007000E
Error in if (rvs != "No RAW file specified!") { :
argument is of length zero
In addition: Warning message:
In system2(exe, stdout = TRUE) :
running command ''/delta/JRC/services/rstudio-home/breidan@delta.europa.eu/.cache/R/rawrr/rawrrassembly/linux-x64/rawrr'' had status 137
sessionInfo()
R version 4.5.0 (2025-04-11)
Platform: x86_64-pc-linux-gnu
Running under: Red Hat Enterprise Linux 9.6 (Plow)

Matrix products: default
BLAS/LAPACK: /usr/lib64/libopenblas-r0.3.26.so; LAPACK version 3.12.0

locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
[4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

time zone: Europe/Rome
tzcode source: system (glibc)

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] rawrr_1.17.2 lubridate_1.9.4 forcats_1.0.0 stringr_1.5.1 dplyr_1.1.4 purrr_1.0.4
[7] readr_2.1.5 tidyr_1.3.1 tibble_3.2.1 tidyverse_2.0.0 ggrepel_0.9.6 ggplot2_3.5.2
[13] magrittr_2.0.3 MUtools_1.4 MASS_7.3-65

loaded via a namespace (and not attached):
[1] vctrs_0.6.5 cli_3.6.4 rlang_1.1.6 stringi_1.8.7 generics_0.1.3
[6] glue_1.8.0 colorspace_2.1-1 hms_1.1.3 scales_1.3.0 grid_4.5.0
[11] munsell_0.5.1 tzdb_0.5.0 lifecycle_1.0.4 compiler_4.5.0 timechange_0.3.0
[16] Rcpp_1.0.14 pkgconfig_2.0.3 rstudioapi_0.17.1 R6_2.6.1 tidyselect_1.2.1
[21] pillar_1.10.2 tools_4.5.0 withr_3.0.2 gtable_0.3.6

[cpanse]

Can you please run

ldd /delta/JRC/services/rstudio-home/breidan@delta.europa.eu/.cache/R/rawrr/rawrrassembly/linux-x64/rawrr

In your bash, sh, or zsh, and send me the output ?

[leoschwarz]

Hi @breidan

The error code at the beginning can indicate a lack of Memory or Storage. Can you verify neither is the problem on your system to rule out this cause?

https://www.hresult.info/FACILITY_WIN32/0x8007000E

[breidan]

@cpanse ,

Can you please run

ldd /delta/JRC/services/rstudio-home/breidan@delta.europa.eu/.cache/R/rawrr/rawrrassembly/linux-x64/rawrr

Here is the output:

linux-vdso.so.1 (0x00007ffdb892a000)
libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f6418e64000)
libdl.so.2 => /lib64/libdl.so.2 (0x00007f6418e5f000)
libz.so.1 => /lib64/libz.so.1 (0x00007f6418e45000)
libm.so.6 => /lib64/libm.so.6 (0x00007f6418d6a000)
librt.so.1 => /lib64/librt.so.1 (0x00007f6418d65000)
libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007f6418d49000)
libstdc++.so.6 => /lib64/libstdc++.so.6 (0x00007f6418a00000)
libc.so.6 => /lib64/libc.so.6 (0x00007f6418600000)
/lib64/ld-linux-x86-64.so.2 (0x00007f641995b000)

[breidan]

Hi @breidan

The error code at the beginning can indicate a lack of Memory or Storage. Can you verify neither is the problem on your system to rule out this cause?

https://www.hresult.info/FACILITY_WIN32/0x8007000E

@leoschwarz,

I can confirm that there is sufficient memory and disk space. When the above error appeared there was 8 % of the memory used and 14 % of the disk space.

[cpanse]

Can you please run

ldd /delta/JRC/services/rstudio-home/breidan@delta.europa.eu/.cache/R/rawrr/rawrrassembly/linux-x64/rawrr

In your bash, sh, or zsh, and send me the output ?

@breidan great. Thank you, and now

/delta/JRC/services/rstudio-home/breidan@delta.europa.eu/.cache/R/rawrr/rawrrassembly/linux-x64/rawrr version

And if that works, please

 /delta/JRC/services/rstudio-home/breidan@delta.europa.eu/.cache/R/rawrr/rawrrassembly/linux-x64/rawrr pathToRawFile.raw index

[breidan]

@cpanse, executing rawrr in the terminal throws the same error:

[breidan@delta.europa.eu@siprapp01p-rstd` linux-x64]$ ./rawrr version

GC heap initialization failed with error 0x8007000E#
Failed to create CoreCLR, HRESULT: 0x8007000E

The server admin has given me more memory access but that did not change anything.

[cpanse]

@breidan, @leoschwarz is on the right track.

At the moment, I have no idea how to help you.

ulimit -Ha
ulimit -Sa

On what kind of system are you working?